Inference of epidemiological parameters from household stratified data

We consider a continuous-time Markov chain model of SIR disease dynamics with two levels of mixing. For this so-called stochastic households model, we provide two methods for inferring the model parameters---governing within-household transmission, recovery, and between-household transmission---from data of the day upon which each individual became infectious and the household in which each infection occurred, as would be available from first few hundred studies. Each method is a form of Bayesian Markov Chain Monte Carlo that allows us to calculate a joint posterior distribution for all parameters and hence the household reproduction number and the early growth rate of the epidemic. The first method performs exact Bayesian inference using a standard data-augmentation approach; the second performs approximate Bayesian inference based on a likelihood approximation derived from branching processes. These methods are compared for computational efficiency and posteriors from each are compared. The branching process is shown to be an excellent approximation and remains computationally efficient as the amount of data is increased

Inverse approach to Einstein's equations for fluids with vanishing anisotropic stress tensor

We expand previous work on an inverse approach to Einstein Field Equations where we include fluids with energy flux and consider the vanishing of the anisotropic stress tensor. We consider the approach using warped product spacetimes of class $B_1$. Although restricted, these spacetimes include many exact solutions of interest to compact object studies and to cosmological models studies. The question explored here is as follows: given a spacetime metric, what fluid flow (timelike congruence), if any, could generate the spacetime via Einstein's equations. We calculate the flow from the condition of a vanishing anisotropic stress tensor and give results in terms of the metric functions in the three canonical types of coordinates. A condition for perfect fluid sources is also provided. The framework developed is algorithmic and suited for the study and validation of exact solutions using computer algebra systems. The framework can be applied to solutions in comoving and non-comoving frames of reference, and examples in different types of coordinates are worked out.Comment: 15 pages, matches version to appear in Phys.Rev.

Evaluation of a non-visual auditory choropleth and travel map viewer

Presented at the 27th International Conference on Auditory Display (ICAD 2022) 24-27 June 2022, Virtual conference.The auditory virtual reality interface of Audiom, a web-based map viewer, was evaluated by thirteen blind participants. In Audiom, the user is an avatar that navigates, using the arrow keys, through geographic data, as if they are playing a first-person, egocentric game. The research questions were: What will make blind users want to use Audiom maps? And Can participants demonstrate basic acquisition of spatial knowledge after viewing an auditory map? A dynamic choropleth map of state-level US COVID-19 data, and a detailed OpenStreetMap powered travel map, were evaluated. All participants agreed they wanted more maps of all kinds, in particular county-level COVID data, and they would use Audiom once some bugs were fixed and their few recommended features were added. Everyone wanted to see Audiom embedded in their existing travel and mapping applications. All participants were able to answer a question evaluating spatial knowledge. Participants also agreed this spatial information was not available in existing applications

d-Amino acid oxidase and serine racemase in human brain: normal distribution and altered expression in schizophrenia

The N-methyl-d-aspartate receptor co-agonist d-serine is synthesized by serine racemase and degraded by d-amino acid oxidase. Both d-serine and its metabolizing enzymes are implicated in N-methyl-d-aspartate receptor hypofunction thought to occur in schizophrenia. We studied d-amino acid oxidase and serine racemase immunohistochemically in several brain regions and compared their immunoreactivity and their mRNA levels in the cerebellum and dorsolateral prefrontal cortex in schizophrenia. d-Amino acid oxidase immunoreactivity was abundant in glia, especially Bergmann glia, of the cerebellum, whereas in prefrontal cortex, hippocampus and substantia nigra, it was predominantly neuronal. Serine racemase was principally glial in all regions examined and demonstrated prominent white matter staining. In schizophrenia, d-amino acid oxidase mRNA was increased in the cerebellum, and as a trend for protein. Serine racemase was increased in schizophrenia in the dorsolateral prefrontal cortex but not in cerebellum, while serine racemase mRNA was unchanged in both regions. Administration of haloperidol to rats did not significantly affect serine racemase or d-amino acid oxidase levels. These findings establish the major cell types wherein serine racemase and d-amino acid oxidase are expressed in human brain and provide some support for aberrant d-serine metabolism in schizophrenia. However, they raise further questions as to the roles of d-amino acid oxidase and serine racemase in both physiological and pathophysiological processes in the brain

Loss of Niemann Pick type C proteins 1 and 2 greatly enhances HIV infectivity and is associated with accumulation of HIV Gag and cholesterol in late endosomes/lysosomes

Abstract Background Cholesterol pathways play an important role at multiple stages during the HIV-1 infection cycle. Here, we investigated the role of cholesterol trafficking in HIV-1 replication utilizing Niemann-Pick Type C disease (NPCD) cells as a model system. Results We used a unique NPC2-deficient cell line (NPCD55) that exhibited Gag accumulation as well as decreased NPC1 expression after HIV infection. Virus release efficiency from NPCD55 cells was similar to that from control cells. However, we observed a 3 to 4-fold enhancement in the infectivity of virus released from these cells. Fluorescence microscopy revealed accumulation and co-localization of Gag proteins with cholesterol in late endosomal/lysosomal (LE/L) compartments of these cells. Virion-associated cholesterol was 4-fold higher in virions produced in NPCD55 cells relative to virus produced in control cells. Treatment of infected NPCD55 cells with the cholesterol efflux-inducing drug TO-9013171 reduced virus infectivity to control levels. Conclusions These results suggest cholesterol trafficking and localization can profoundly affect HIV-1 infectivity by modulating the cholesterol content of the virions.</p

Incomplete Punishment Networks in Public Goods Games: Experimental Evidence

Abundant evidence suggests that high levels of contributions to public goods can be sustained through self-governed monitoring and sanctioning. This experimental study investigates the effectiveness of decentralized sanctioning institutions in alternative punishment networks. Our results show that the structure of punishment network significantly affects allocations to the public good. In addition, we observe that network configurations are more important than punishment capacities for the levels of public good provision, imposed sanctions and economic efficiency. Lastly, we show that targeted revenge is a major driver of anti-social punishment

'The Brick' is not a brick : A comprehensive study of the structure and dynamics of the Central Molecular Zone cloud G0.253+0.016

© 2019 The Author(s) Published by Oxford University Press on behalf of the Royal Astronomical Society.In this paper we provide a comprehensive description of the internal dynamics of G0.253+0.016 (a.k.a. 'the Brick'); one of the most massive and dense molecular clouds in the Galaxy to lack signatures of widespread star formation. As a potential host to a future generation of high-mass stars, understanding largely quiescent molecular clouds like G0.253+0.016 is of critical importance. In this paper, we reanalyse Atacama Large Millimeter Array cycle 0 HNCO $J=4(0,4)-3(0,3)$ data at 3 mm, using two new pieces of software which we make available to the community. First, scousepy, a Python implementation of the spectral line fitting algorithm scouse. Secondly, acorns (Agglomerative Clustering for ORganising Nested Structures), a hierarchical n-dimensional clustering algorithm designed for use with discrete spectroscopic data. Together, these tools provide an unbiased measurement of the line of sight velocity dispersion in this cloud, $\sigma_{v_{los}, {\rm 1D}}=4.4\pm2.1$ kms$^{-1}$, which is somewhat larger than predicted by velocity dispersion-size relations for the Central Molecular Zone (CMZ). The dispersion of centroid velocities in the plane of the sky are comparable, yielding $\sigma_{v_{los}, {\rm 1D}}/\sigma_{v_{pos}, {\rm 1D}}\sim1.2\pm0.3$. This isotropy may indicate that the line-of-sight extent of the cloud is approximately equivalent to that in the plane of the sky. Combining our kinematic decomposition with radiative transfer modelling we conclude that G0.253+0.016 is not a single, coherent, and centrally-condensed molecular cloud; 'the Brick' is not a \emph{brick}. Instead, G0.253+0.016 is a dynamically complex and hierarchically-structured molecular cloud whose morphology is consistent with the influence of the orbital dynamics and shear in the CMZ.Peer reviewedFinal Accepted Versio